International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data

By Junjun Zhang, J. Baran, A. Cros, J. Guberman, Syed Haider, J. Hsu, Yong Liang, E. Rivkin, Jianxin Wang, Brett Whitty and 3 more. Database J. Biol. Databases Curation, 2011

625 citations recorded by the source corpus.

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal. Database URL: http://dcc.icgc.org

Subfields: Cancer Research, Molecular Biology, Oncology

View Paper: https://www.semanticscholar.org/paper/a91365e58cec221d4178b304b399a8ff6eedba81

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Citations in the corpus

BioMart: driving a paradigm change in biological data management (2011, background): “…introduced a new innovative way of creating large multi-database repositories that avoid the need to store all the data in a single location (2), and finally it proved that large-scale projects involving next generation sequencing data can be managed efficiently in a distributed environment (3).”
The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery (2015, methodology): “, 2013] or other large data centers such as those employed for the International Cancer Genome Consortium (ICGC) [Zhang et al., 2011] and the Cancer GenomeAtlas (TCGA) [Weinstein et al.”
Sangerbox: A comprehensive, interaction‐friendly clinical bioinformatics analysis platform (2022, methodology): “These data are derived from The Cancer Genome Atlas (TCGA) [22], International Cancer Genome Consortium (ICGC) [23], Gene Expression Omnibus (GEO) [24], and other databases with clinical follow ‐ up information, clinical data, mutation data, and expression profile data.”
The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data (2012, methodology): “The cBio portal complements existing tools, including the TCGA and ICGC data portals (13), the IGV (7), the UCSC Cancer Genomics Browser (14), and IntOGen (15) by offering a unique focus on analyzing discrete genomic events across integrated data types, ease of use, support for exploratory data…”